Hepatitis C virus (HCV) is an important human pathogen that is strongly associated with post transfusion hepatitis as well as sporadic non-A, non-B hepatitis. Recently, HCV cDNA was cloned and its genome sequenced by others. A region of the predicted polyprotein sequence was found to share similarity with a non-structural protein encoded by dengue virus, a member of the flavivirus family. We found, using computer-assisted analysis, that HCV shares an even greater degree of protein sequence similarity with members of the pestivirus group (i.e., bovine viral diarrhea virus and hog cholera virus) which are thought to be distantly related to the flaviviruses. In addition, we found that HCV shares significant protein sequence similarity with the polyproteins encoded by members of the picornavirus-like and alphavirus-like plant virus supergroups. These data suggest that HCV may be evolutionarily related to both plant and animal viruses. PCR amplification was used to study the pathogenesis of HCV infection in patients and experimentally infected primates. An unexpected finding was the observation that HCV replication begins as early as three days following experimental infection of chimpanzees.